Title: Fit a spatial occupancy model via Gibbs sampling
Diff between stocc versions 1.0-7 dated 2012-11-27 and 1.23 dated 2014-07-29
Description: Fit a spatial-temporal occupancy models using
a probit formulation instead of a traditional logit
model.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson
DESCRIPTION | 16 -
MD5 | 28 +-
NAMESPACE | 2
R/icar.Q.R | 3
R/spatial.occupancy.R | 531 +++++++++++++++++++++++------------------------
R/stocc-package.R | 104 +++------
demo/00Index | 2
demo/simDataMCMC.R | 14 +
man/habData.Rd | 8
man/icar.Q.Rd | 28 +-
man/make.so.data.Rd | 51 ++--
man/occupancyData.Rd | 29 +-
man/spatial.occupancy.Rd | 193 +++++++----------
man/stocc-package.Rd | 23 --
man/visitData.Rd | 20 -
15 files changed, 505 insertions(+), 547 deletions(-)
Title: Easy interface to advanced PostgreSQL features
Diff between rpg versions 1.0 dated 2014-07-24 and 1.1 dated 2014-07-29
Description: Allows ad hoc queries and reading and
writing data frames to and from a database.
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/rpg.R | 10 ++--------
man/connection.Rd | 6 ------
man/rpg-package.Rd | 4 ++--
src/rpg.cpp | 3 +--
src/rpg.h | 16 +++++++++-------
7 files changed, 25 insertions(+), 36 deletions(-)
Title: Parameterized queries extension for RODBC
Diff between RODBCext versions 0.2.2 dated 2014-07-07 and 0.2.3 dated 2014-07-29
Description: An extension for RODBC package adding support for parameterized
queries
Author: Mateusz Zoltak [aut, cre],
Brian Ripley [aut],
Michael Lapsley [aut]
Maintainer: Mateusz Zoltak
RODBCext |only
1 file changed
Title: Fit statistic for binary dependent variable models
Diff between heatmapFit versions 2.0 dated 2014-07-22 and 2.0.1 dated 2014-07-29
Description: Generates a fit plot for diagnosing misspecification in models of
binary dependent variables, and calculates the related heatmap fit
statistic (Esarey and Pierce, 2012).
Author: Justin Esarey [aut, cre],
Andrew Pierce [aut],
Jericho Du [aut]
Maintainer: Justin Esarey
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/heatmap.fit.R | 6 +++---
man/heatmap.fit.Rd | 4 ++--
4 files changed, 11 insertions(+), 11 deletions(-)
Title: Psychometric Mixture Models
Diff between psychomix versions 1.1-0 dated 2013-12-10 and 1.1-1 dated 2014-07-29
Description: Psychometric mixture models based on flexmix infrastructure. At the moment Rasch mixture models
with different parametrizations of the score distribution (saturated vs. mean/variance specification)
and Bradley-Terry mixture models are implemented. Both mixture models can be estimated with or without
concomitant variables. See vignette("raschmix", package = "psychomix") for details on the Rasch mixture
models.
Author: Hannah Frick [aut, cre],
Carolin Strobl [aut],
Friedrich Leisch [aut],
Achim Zeileis [aut]
Maintainer: Hannah Frick
DESCRIPTION | 8
MD5 | 36
R/raschmix.R | 13
build/vignette.rds |binary
inst/CITATION | 21
inst/doc/raschmix.pdf |binary
inst/doc/scores.R | 258 ++---
inst/doc/scores.Rnw | 1468 +++++++++++++++++++++-------------
inst/doc/scores.pdf |binary
inst/doc/scoresim.rda |binary
man/effectsplot.Rd | 2
man/raschmix.Rd | 29
tests/Examples/psychomix-Ex.Rout.save | 77 -
tests/test.Rout.save | 44 -
vignettes/psychomix.bib | 111 ++
vignettes/raschmix.Rout.save | 138 +--
vignettes/scores.Rnw | 1468 +++++++++++++++++++++-------------
vignettes/scores.Rout.save | 259 +----
vignettes/scoresim.rda |binary
19 files changed, 2298 insertions(+), 1634 deletions(-)
Title: Network meta-analysis with R
Diff between netmeta versions 0.5-0 dated 2014-06-24 and 0.6-0 dated 2014-07-29
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 9
MD5 | 20 +-
NAMESPACE | 2
NEWS | 43 ++++
R/forest.netmeta.R | 26 ++
R/netgraph.R | 456 +++++++++++++++++++++++++++++++++++++++++---------
R/netmeta.R | 14 +
R/nma.ruecker.R | 55 +++++-
R/nodedist.R |only
R/stress.R |only
man/forest.netmeta.Rd | 8
man/netgraph.Rd | 218 ++++++++++++++++++++---
12 files changed, 725 insertions(+), 126 deletions(-)
Title: Reading, manipulation and writing BAM (Binary alignment) files.
Diff between rbamtools versions 2.9.11 dated 2014-06-24 and 2.9.14 dated 2014-07-29
Description: This package provides an interface to functions of the
'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers
ChangeLog |only
DESCRIPTION | 7
MD5 | 27
NEWS |only
R/rbamtools.r | 5619 +++++++++++++++++++++++++++---------------------
build/vignette.rds |binary
inst/doc/rbamtools.R | 292 +-
inst/doc/rbamtools.Rnw | 1133 ++++++---
inst/doc/rbamtools.pdf |binary
man/alignDepth-class.Rd | 36
man/bamReader-class.Rd | 25
man/getRefData.Rd |only
man/nucStats.Rd | 3
src/samtools/bam.c | 2
tests |only
vignettes/rbamtools.Rnw | 1133 ++++++---
16 files changed, 4988 insertions(+), 3289 deletions(-)
Title: General network (HTTP/FTP/...) client interface for R
Diff between RCurl versions 1.95-4.2 dated 2014-07-28 and 1.95-4.3 dated 2014-07-29
Description: The package allows one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/Makevars.win | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Probabilities for Pedigrees given DNA data
Diff between Familias versions 1.2 dated 2013-04-17 and 2.0 dated 2014-07-29
Description:
This package represents an interface to the core Familias functions (www.familias.name),
which are programmed in C++. The interface is completely changed from version 1.2 of this
package, so programs dependent on the old functions should continue to use that version.
Author: Petter Mostad and Thore Egeland
Maintainer: Petter Mostad
Familias-1.2/Familias/R/Familias.R |only
Familias-1.2/Familias/R/postFamilias.R |only
Familias-1.2/Familias/R/preFamilias.R |only
Familias-1.2/Familias/man/AddAlleleSystem.Rd |only
Familias-1.2/Familias/man/AddDNAObservation.Rd |only
Familias-1.2/Familias/man/AddExtraPerson.Rd |only
Familias-1.2/Familias/man/AddFixedRelation.Rd |only
Familias-1.2/Familias/man/AddPedigree.Rd |only
Familias-1.2/Familias/man/AddPerson.Rd |only
Familias-1.2/Familias/man/AddRelation.Rd |only
Familias-1.2/Familias/man/EditAlleleSystem.Rd |only
Familias-1.2/Familias/man/GeneratePedigrees.Rd |only
Familias-1.2/Familias/man/GetNumberOfExtraFemales.Rd |only
Familias-1.2/Familias/man/GetNumberOfExtraMales.Rd |only
Familias-1.2/Familias/man/GetNumberOfPedigrees.Rd |only
Familias-1.2/Familias/man/GetNumberOfSystems.Rd |only
Familias-1.2/Familias/man/GetParents.Rd |only
Familias-1.2/Familias/man/GetPedigree.Rd |only
Familias-1.2/Familias/man/GetProbabilities.Rd |only
Familias-1.2/Familias/man/GetSizeOfPedigree.Rd |only
Familias-1.2/Familias/man/NewFamilias.Rd |only
Familias-1.2/Familias/man/RemoveAlleleSystem.Rd |only
Familias-1.2/Familias/man/RemoveDNAObservation.Rd |only
Familias-1.2/Familias/man/RemoveExtraPerson.Rd |only
Familias-1.2/Familias/man/RemoveFixedRelation.Rd |only
Familias-1.2/Familias/man/RemovePedigree.Rd |only
Familias-1.2/Familias/man/RemovePerson.Rd |only
Familias-1.2/Familias/man/RemoveRelation.Rd |only
Familias-1.2/Familias/man/postFamilias.Rd |only
Familias-1.2/Familias/man/preFamilias.Rd |only
Familias-2.0/Familias/DESCRIPTION | 19
Familias-2.0/Familias/MD5 | 70 -
Familias-2.0/Familias/NAMESPACE | 31
Familias-2.0/Familias/R/ConvertPed.R |only
Familias-2.0/Familias/R/FamiliasLocus.R |only
Familias-2.0/Familias/R/FamiliasPosterior.R |only
Familias-2.0/Familias/R/FamiliasPrior.R |only
Familias-2.0/Familias/man/ConvertPed.Rd |only
Familias-2.0/Familias/man/Familias-package.Rd | 64 -
Familias-2.0/Familias/man/FamiliasLocus.Rd |only
Familias-2.0/Familias/man/FamiliasPosterior.Rd |only
Familias-2.0/Familias/man/FamiliasPrior.Rd |only
Familias-2.0/Familias/src/FamInterface.cpp | 61 -
Familias-2.0/Familias/src/FamInterface.h | 258 ++--
Familias-2.0/Familias/src/PedigreeSet.cpp | 3
Familias-2.0/Familias/src/PedigreeSet.h | 8
Familias-2.0/Familias/src/aldata.cpp | 100 -
Familias-2.0/Familias/src/aldata.h | 14
Familias-2.0/Familias/src/alsys.cpp | 996 ++-----------------
Familias-2.0/Familias/src/alsys.h | 71 -
Familias-2.0/Familias/src/main.cpp | 327 +++---
Familias-2.0/Familias/src/pater.cpp | 22
Familias-2.0/Familias/src/pater.h | 18
Familias-2.0/Familias/src/read.cpp | 106 --
Familias-2.0/Familias/src/read.h | 4
55 files changed, 655 insertions(+), 1517 deletions(-)
Title: Pheno2Geno - Generating genetic markers and maps from molecular
phenotypes
Diff between pheno2geno versions 1.2.0 dated 2014-06-10 and 1.2.1 dated 2014-07-29
Description: Pheno2Geno is an R package for the computational generation genetic markers and maps from molecular phenotypes
Author: Konrad Zych
Maintainer: Konrad Zych
DESCRIPTION | 6
MD5 | 14 -
R/cross.saturate.R | 14 -
R/power.plot.R | 3
data/yeastCross.rda |binary
data/yeastPopulation.rda |binary
tests/mycross.csv | 378 ++++++++---------------------------------------
tests/test_analysis.R | 10 -
8 files changed, 92 insertions(+), 333 deletions(-)
Title: Robust Ordinal Regression UTADIS
Diff between rorutadis versions 0.1.1 dated 2014-04-11 and 0.1.3 dated 2014-07-29
Description: Implementation of Robust Ordinal Regression for value-based sorting with some extensions and additional tools. It is a novel Multiple-Criteria Decision Aiding (MCDA) framework.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek
rorutadis-0.1.1/rorutadis/README.md |only
rorutadis-0.1.3/rorutadis/DESCRIPTION | 8
rorutadis-0.1.3/rorutadis/MD5 | 81 ++++------
rorutadis-0.1.3/rorutadis/NAMESPACE | 2
rorutadis-0.1.3/rorutadis/R/main.R | 58 ++++++-
rorutadis-0.1.3/rorutadis/R/model.R | 1
rorutadis-0.1.3/rorutadis/R/parameters.R | 2
rorutadis-0.1.3/rorutadis/R/postFactumAnalysis.R | 76 +++++++--
rorutadis-0.1.3/rorutadis/R/problem.R | 2
rorutadis-0.1.3/rorutadis/inst/tests/test-main.R | 30 +++
rorutadis-0.1.3/rorutadis/man/addAssignmentPairwiseAtLeastComparisons.Rd | 23 +-
rorutadis-0.1.3/rorutadis/man/addAssignmentPairwiseAtMostComparisons.Rd | 20 +-
rorutadis-0.1.3/rorutadis/man/addAssignmentsLB.Rd | 11 -
rorutadis-0.1.3/rorutadis/man/addAssignmentsUB.Rd | 14 -
rorutadis-0.1.3/rorutadis/man/addMaximalClassCardinalities.Rd | 12 -
rorutadis-0.1.3/rorutadis/man/addMinimalClassCardinalities.Rd | 12 -
rorutadis-0.1.3/rorutadis/man/buildProblem.Rd | 25 +--
rorutadis-0.1.3/rorutadis/man/calculateAssignments.Rd | 25 +--
rorutadis-0.1.3/rorutadis/man/calculateExtremeClassCardinalities.Rd | 19 +-
rorutadis-0.1.3/rorutadis/man/checkConsistency.Rd | 7
rorutadis-0.1.3/rorutadis/man/compareAssignments.Rd | 22 +-
rorutadis-0.1.3/rorutadis/man/deteriorateAssignment.Rd | 37 +---
rorutadis-0.1.3/rorutadis/man/drawUtilityPlots.Rd | 40 ++--
rorutadis-0.1.3/rorutadis/man/explainAssignment.Rd | 34 +---
rorutadis-0.1.3/rorutadis/man/findRepresentativeFunction.Rd | 33 ++--
rorutadis-0.1.3/rorutadis/man/getAssignments.Rd | 13 -
rorutadis-0.1.3/rorutadis/man/getCharacteristicPoints.Rd | 18 --
rorutadis-0.1.3/rorutadis/man/getMarginalUtilities.Rd | 15 -
rorutadis-0.1.3/rorutadis/man/getPreferentialCore.Rd | 10 -
rorutadis-0.1.3/rorutadis/man/getRestrictions.Rd | 13 -
rorutadis-0.1.3/rorutadis/man/getThresholds.Rd | 17 --
rorutadis-0.1.3/rorutadis/man/improveAssignment.Rd | 34 +---
rorutadis-0.1.3/rorutadis/man/investigateUtility.Rd | 34 ++--
rorutadis-0.1.3/rorutadis/man/mergeAssignments.Rd | 53 +++---
rorutadis-0.1.3/rorutadis/man/removeAssignmentPairwiseAtLeastComparisons.Rd | 23 +-
rorutadis-0.1.3/rorutadis/man/removeAssignmentPairwiseAtMostComparisons.Rd | 23 +-
rorutadis-0.1.3/rorutadis/man/removeAssignmentsLB.Rd | 22 +-
rorutadis-0.1.3/rorutadis/man/removeAssignmentsUB.Rd | 22 +-
rorutadis-0.1.3/rorutadis/man/removeConstraintsByRestrictions.Rd | 19 --
rorutadis-0.1.3/rorutadis/man/removeMaximalClassCardinalities.Rd | 21 +-
rorutadis-0.1.3/rorutadis/man/removeMinimalClassCardinalities.Rd | 21 +-
rorutadis-0.1.3/rorutadis/man/rorutadis-package.Rd | 4
42 files changed, 510 insertions(+), 446 deletions(-)
Title: an R package for genetic analysis of populations with mixed
reproduction
Diff between poppr versions 1.1.1 dated 2014-07-27 and 1.1.2 dated 2014-07-29
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar
Maintainer: Zhian N. Kamvar
poppr-1.1.1/poppr/inst/README |only
poppr-1.1.1/poppr/vignettes/figure/Aeut_MLG_Ahena1.pdf |only
poppr-1.1.1/poppr/vignettes/figure/Aeut_MLG_Ahena2.pdf |only
poppr-1.1.1/poppr/vignettes/figure/unnamed-chunk-8.pdf |only
poppr-1.1.1/poppr/vignettes/figure/unnamed-chunk-9.pdf |only
poppr-1.1.2/poppr/DESCRIPTION | 6
poppr-1.1.2/poppr/MD5 | 73 +++++------
poppr-1.1.2/poppr/NEWS | 6
poppr-1.1.2/poppr/README.md | 2
poppr-1.1.2/poppr/inst/doc/algo.Rnw | 4
poppr-1.1.2/poppr/inst/doc/algo.pdf |binary
poppr-1.1.2/poppr/inst/doc/poppr_manual.Rnw | 2
poppr-1.1.2/poppr/inst/doc/poppr_manual.pdf |binary
poppr-1.1.2/poppr/src/poppr_distance.c | 73 +++++------
poppr-1.1.2/poppr/vignettes/algo.Rnw | 4
poppr-1.1.2/poppr/vignettes/figure/Aeut_MLG_Ahena.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/Aeut_MLG_black.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/Aeut_MLG_title.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/bd_histogram.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/bruvo_msn.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/bruvo_tree.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/ex_data_picture.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/ggplotchart.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/greycurve_normal.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/greycurve_small_heavy.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/greywidth_inverse.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/greywidth_large_heavy.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/initializing_poppr.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/mantel.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/mlgbarplot.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/mlgrareplot.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/popcompare_bruvo2.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/poppr_msn_fig.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/subnor.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/unnamed-chunk-3.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/unnamed-chunk-4.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/unnamed-chunk-5.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/unnamed-chunk-6.pdf |binary
poppr-1.1.2/poppr/vignettes/figure/unnamed-chunk-7.pdf |binary
poppr-1.1.2/poppr/vignettes/poppr_manual.Rnw | 2
40 files changed, 85 insertions(+), 87 deletions(-)
Title: R interface to the phreeqc geochemical modeling program
Diff between phreeqc versions 1.0-8847 dated 2014-07-16 and 1.0-8877 dated 2014-07-29
Description: R interface to PHREEQC (Version 3). PHREEQC is a geochemical
modeling program developed by the US Geological Survey that is designed
to perform a wide variety of aqueous geochemical calculations,
including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions
from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,
R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton
DESCRIPTION | 6 -
MD5 | 162 ++++++++++++++++++------------------
NAMESPACE | 2
R/phreeqc.R | 2
man/Amm.dat.Rd | 18 ++--
man/ex1.Rd | 32 +++----
man/ex10.Rd | 44 ++++-----
man/ex11.Rd | 42 ++++-----
man/ex12.Rd | 58 ++++++------
man/ex13.Rd | 41 ++++-----
man/ex14.Rd | 51 +++++------
man/ex15.Rd | 46 ++++------
man/ex15.dat.Rd | 15 +--
man/ex16.Rd | 52 +++++------
man/ex17.Rd | 51 +++++------
man/ex18.Rd | 71 +++++++--------
man/ex19.Rd | 37 ++++----
man/ex2.Rd | 28 +++---
man/ex20.Rd | 56 +++++-------
man/ex21.Rd | 51 +++++------
man/ex22.Rd | 45 ++++------
man/ex3.Rd | 50 +++++------
man/ex4.Rd | 53 +++++------
man/ex5.Rd | 40 ++++----
man/ex6.Rd | 35 +++----
man/ex7.Rd | 60 ++++++-------
man/ex8.Rd | 37 ++++----
man/ex9.Rd | 61 ++++++-------
man/iso.dat.Rd | 17 ++-
man/llnl.dat.Rd | 16 +--
man/minteq.dat.Rd | 13 +-
man/minteq.v4.dat.Rd | 13 +-
man/phrAccumulateLine.Rd | 11 +-
man/phrClearAccumulatedLines.Rd | 10 +-
man/phrGetAccumulatedLines.Rd | 5 -
man/phrGetComponentList.Rd | 4
man/phrGetDumpFileName.Rd | 16 +--
man/phrGetDumpFileOn.Rd | 11 +-
man/phrGetDumpStrings.Rd | 15 +--
man/phrGetDumpStringsOn.Rd | 11 +-
man/phrGetErrorFileName.Rd | 17 +--
man/phrGetErrorFileOn.Rd | 11 +-
man/phrGetErrorStrings.Rd | 27 ++----
man/phrGetErrorStringsOn.Rd | 11 +-
man/phrGetLogFileName.Rd | 14 +--
man/phrGetLogFileOn.Rd | 11 +-
man/phrGetLogStrings.Rd | 11 +-
man/phrGetLogStringsOn.Rd | 11 +-
man/phrGetOutputFileName.Rd | 14 +--
man/phrGetOutputFileOn.Rd | 11 +-
man/phrGetOutputStrings.Rd | 11 +-
man/phrGetOutputStringsOn.Rd | 11 +-
man/phrGetSelectedOutput.Rd | 29 ++----
man/phrGetSelectedOutputFileName.Rd | 14 +--
man/phrGetWarningStrings.Rd | 13 +-
man/phrLoadDatabase.Rd | 6 -
man/phrLoadDatabaseString.Rd | 8 -
man/phrRunAccumulated.Rd | 24 ++---
man/phrRunFile.Rd | 5 -
man/phrRunString.Rd | 17 +--
man/phrSetDumpFileName.Rd | 18 ++--
man/phrSetDumpFileOn.Rd | 19 ++--
man/phrSetDumpStringsOn.Rd | 21 ++--
man/phrSetErrorFileName.Rd | 16 +--
man/phrSetErrorFileOn.Rd | 22 ++--
man/phrSetErrorStringsOn.Rd | 24 ++---
man/phrSetLogFileName.Rd | 20 ++--
man/phrSetLogFileOn.Rd | 23 ++---
man/phrSetLogStringsOn.Rd | 21 ++--
man/phrSetOutputFileName.Rd | 19 ++--
man/phrSetOutputFileOn.Rd | 21 ++--
man/phrSetOutputStringsOn.Rd | 21 ++--
man/phrSetSelectedOutputFileName.Rd | 19 +---
man/phrSetSelectedOutputFileOn.Rd | 21 ++--
man/phreeqc-package.Rd | 25 ++---
man/phreeqc.dat.Rd | 16 +--
man/pitzer.dat.Rd | 16 +--
man/sit.dat.Rd | 16 +--
man/wateq4f.dat.Rd | 14 +--
src/phreeqcpp/basicsubs.cpp | 2
src/phreeqcpp/tidy.cpp | 5 -
src/phreeqcpp/utilities.cpp | 2
82 files changed, 992 insertions(+), 1053 deletions(-)
Title: Non-clustered heatmap alternatives
Diff between NeatMap versions 0.3.6.1 dated 2013-11-01 and 0.3.6.2 dated 2014-07-29
Description: NeatMap is a package to create heatmap like plots in 2 and
3 dimensions, without the need for cluster analysis. Like the
heatmap, the plots created by NeatMap display both a
dimensionally reduced representation of the data as well as the
data itself. They are intended to be used in conjunction with
dimensional reduction techniques such as PCA.
Author: Satwik Rajaram and Yoshi Oono
Maintainer: Satwik Rajaram
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NAMESPACE | 3 ++-
man/heatmap1.Rd | 3 ++-
4 files changed, 11 insertions(+), 9 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 3.7-0 dated 2014-07-11 and 3.7-1 dated 2014-07-29
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NEWS | 18 ++++++++++++++++--
R/forest.meta.R | 36 ++++++++++++++++++++++++------------
man/forest.Rd | 44 ++++++++++++++++++++++++++++++++++++++++++++
5 files changed, 92 insertions(+), 22 deletions(-)
Title: Local Correlation, Spatial Inequalities and other tools
Diff between lctools versions 0.1-2 dated 2014-04-26 and 0.1-3 dated 2014-07-29
Description: Local Correlation Coefficients (Local Pearson and Geographically Weighted Pearson), Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics)
Author: Stamatis Kalogirou
Maintainer: Stamatis Kalogirou
DESCRIPTION | 12 ++++++------
MD5 | 20 +++++++++++++-------
R/mc_correl.R |only
R/mc_spGini.R |only
R/moransI.R |only
R/spGini.R | 3 +--
man/acc.Rd | 3 +--
man/gw_variable.Rd | 8 ++------
man/lcorrel.Rd | 6 ++----
man/lctools-package.Rd | 23 ++++++++++++++++-------
man/mc_correl.Rd |only
man/mc_spGini.Rd |only
man/moransI.Rd |only
man/spGini.Rd | 4 ++--
14 files changed, 43 insertions(+), 36 deletions(-)
Title: Drawing Hasse diagram
Diff between hasseDiagram versions 0.1 dated 2014-04-12 and 0.1.1 dated 2014-07-29
Description: Drawing Hasse diagram - visualization of transitive reduction of a finite partially ordered set.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek
hasseDiagram-0.1.1/hasseDiagram/DESCRIPTION | 8 +-
hasseDiagram-0.1.1/hasseDiagram/MD5 | 13 +--
hasseDiagram-0.1.1/hasseDiagram/NAMESPACE | 2
hasseDiagram-0.1.1/hasseDiagram/R/hasse.R | 9 +-
hasseDiagram-0.1.1/hasseDiagram/man/generateRandomData.Rd | 12 +--
hasseDiagram-0.1.1/hasseDiagram/man/hasse.Rd | 45 +++++-------
hasseDiagram-0.1.1/hasseDiagram/man/hasseDiagram-package.Rd | 4 -
hasseDiagram-0.1/hasseDiagram/README.md |only
8 files changed, 48 insertions(+), 45 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Diff between EpiModel versions 1.0 dated 2014-06-09 and 1.0.1 dated 2014-07-29
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Li Wang [ctb]
Maintainer: Samuel Jenness
EpiModel-1.0.1/EpiModel/DESCRIPTION | 14
EpiModel-1.0.1/EpiModel/MD5 | 128 +-
EpiModel-1.0.1/EpiModel/NAMESPACE | 4
EpiModel-1.0.1/EpiModel/NEWS | 43
EpiModel-1.0.1/EpiModel/R/EpiModel-package.r | 147 +-
EpiModel-1.0.1/EpiModel/R/as.data.frame.R | 124 +-
EpiModel-1.0.1/EpiModel/R/control.R | 509 ++++------
EpiModel-1.0.1/EpiModel/R/crosscheck.R | 226 ++--
EpiModel-1.0.1/EpiModel/R/dcm.R | 122 +-
EpiModel-1.0.1/EpiModel/R/dcm.mods.R | 200 +--
EpiModel-1.0.1/EpiModel/R/icm.R | 122 +-
EpiModel-1.0.1/EpiModel/R/icm.mod.init.R | 84 -
EpiModel-1.0.1/EpiModel/R/icm.mod.status.R | 70 -
EpiModel-1.0.1/EpiModel/R/icm.mod.vital.R | 69 -
EpiModel-1.0.1/EpiModel/R/icm.utils.R | 80 -
EpiModel-1.0.1/EpiModel/R/init.R | 232 ++--
EpiModel-1.0.1/EpiModel/R/merge.R | 126 +-
EpiModel-1.0.1/EpiModel/R/modules.icm.R |only
EpiModel-1.0.1/EpiModel/R/modules.net.R | 114 +-
EpiModel-1.0.1/EpiModel/R/net.mod.init.R | 168 +--
EpiModel-1.0.1/EpiModel/R/net.mod.simnet.R | 46
EpiModel-1.0.1/EpiModel/R/net.mod.status.R | 182 +--
EpiModel-1.0.1/EpiModel/R/net.mod.vital.R | 518 ++++------
EpiModel-1.0.1/EpiModel/R/net.utils.R | 569 +++++------
EpiModel-1.0.1/EpiModel/R/netdx.R | 216 ++--
EpiModel-1.0.1/EpiModel/R/netest.R | 217 ++--
EpiModel-1.0.1/EpiModel/R/netsim.R | 170 +--
EpiModel-1.0.1/EpiModel/R/param.R | 466 ++++-----
EpiModel-1.0.1/EpiModel/R/plot.R | 1201 +++++++++++++-----------
EpiModel-1.0.1/EpiModel/R/print.r | 170 +--
EpiModel-1.0.1/EpiModel/R/saveout.R | 93 +
EpiModel-1.0.1/EpiModel/R/shiny.R | 34
EpiModel-1.0.1/EpiModel/R/summary.R | 258 ++---
EpiModel-1.0.1/EpiModel/R/utils.R | 124 +-
EpiModel-1.0.1/EpiModel/R/verbose.R | 85 -
EpiModel-1.0.1/EpiModel/R/zzz.R | 45
EpiModel-1.0.1/EpiModel/build/vignette.rds |binary
EpiModel-1.0.1/EpiModel/inst/doc/Intro.R | 8
EpiModel-1.0.1/EpiModel/inst/doc/Intro.Rnw | 42
EpiModel-1.0.1/EpiModel/inst/doc/Intro.pdf |binary
EpiModel-1.0.1/EpiModel/man/EpiModel-package.Rd | 120 +-
EpiModel-1.0.1/EpiModel/man/control.net.Rd | 18
EpiModel-1.0.1/EpiModel/man/dcm.Rd | 2
EpiModel-1.0.1/EpiModel/man/deaths.net.Rd |only
EpiModel-1.0.1/EpiModel/man/epiweb.Rd | 6
EpiModel-1.0.1/EpiModel/man/icm.Rd | 2
EpiModel-1.0.1/EpiModel/man/init.dcm.Rd | 12
EpiModel-1.0.1/EpiModel/man/init.icm.Rd | 12
EpiModel-1.0.1/EpiModel/man/init.net.Rd | 10
EpiModel-1.0.1/EpiModel/man/modules.icm.Rd |only
EpiModel-1.0.1/EpiModel/man/modules.net.Rd | 90 -
EpiModel-1.0.1/EpiModel/man/netest.Rd | 10
EpiModel-1.0.1/EpiModel/man/param.dcm.Rd | 16
EpiModel-1.0.1/EpiModel/man/param.icm.Rd | 16
EpiModel-1.0.1/EpiModel/man/param.net.Rd | 18
EpiModel-1.0.1/EpiModel/man/plot.dcm.Rd | 2
EpiModel-1.0.1/EpiModel/man/plot.icm.Rd | 4
EpiModel-1.0.1/EpiModel/man/plot.netdx.Rd | 12
EpiModel-1.0.1/EpiModel/man/plot.netsim.Rd | 10
EpiModel-1.0.1/EpiModel/man/summary.netsim.Rd | 2
EpiModel-1.0.1/EpiModel/tests |only
EpiModel-1.0.1/EpiModel/vignettes/Intro.Rnw | 42
EpiModel-1.0/EpiModel/man/deaths_inf.net.Rd |only
EpiModel-1.0/EpiModel/man/deaths_rec.net.Rd |only
EpiModel-1.0/EpiModel/man/deaths_sus.net.Rd |only
65 files changed, 3794 insertions(+), 3636 deletions(-)